Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:44 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 2228/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
wateRmelon 2.11.2 (landing page) Leo C Schalkwyk
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the wateRmelon package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/wateRmelon.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: wateRmelon |
Version: 2.11.2 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wateRmelon.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wateRmelon_2.11.2.tar.gz |
StartedAt: 2024-08-27 00:08:46 -0400 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 00:16:03 -0400 (Tue, 27 Aug 2024) |
EllapsedTime: 436.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: wateRmelon.Rcheck |
Warnings: 5 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wateRmelon.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wateRmelon_2.11.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/wateRmelon.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘wateRmelon/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘wateRmelon’ version ‘2.11.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'Biobase', 'limma', 'matrixStats', 'methylumi', 'lumi', 'ROC', 'IlluminaHumanMethylation450kanno.ilmn12.hg19', 'illuminaio' Adding so many packages to the search path is excessive and importing selectively is preferable. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘wateRmelon’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘Biobase’ A package should be listed in only one of these fields. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘R.utils’ Packages in Depends field not imported from: ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’ ‘matrixStats’ ‘methylumi’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported objects imported by ':::' calls: ‘minfi:::.annoGet’ ‘minfi:::.availableAnnotation’ ‘minfi:::.isRGOrStop’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE readPepo: warning in dir(idatdir, patt = "idat"): partial argument match of 'patt' to 'pattern' .adjusted_normalizeFunnorm450k : unbiased_normalizeQuantiles: no visible global function definition for ‘colQuantiles’ .adjusted_normalizeFunnorm450k: no visible global function definition for ‘getMeth’ .adjusted_normalizeFunnorm450k: no visible global function definition for ‘getUnmeth’ .adjusted_normalizeFunnorm450k: no visible global function definition for ‘assay<-’ .buildControlMatrix450k: no visible global function definition for ‘colMeans2’ .extractFromRGSet450k: no visible global function definition for ‘getProbeInfo’ .extractFromRGSet450k: no visible global function definition for ‘getRed’ .extractFromRGSet450k: no visible global function definition for ‘getGreen’ .extractFromRGSet450k: no visible global function definition for ‘getOOB’ .extractFromRGSet450k: no visible global function definition for ‘colQuantiles’ .getFunnormIndices: no visible global function definition for ‘getProbeType’ .getFunnormIndices: no visible global function definition for ‘seqnames’ .isMatrixBacked: no visible global function definition for ‘assays’ .regularizeQuantiles: no visible global function definition for ‘colCummaxs’ .returnFit: no visible global function definition for ‘rowMeans2’ IDATsToMatrices2: no visible global function definition for ‘.mclapply’ NChannelSetToMethyLumiSet2: no visible global function definition for ‘betas’ NChannelSetToMethyLumiSet2: no visible global function definition for ‘methylated’ NChannelSetToMethyLumiSet2: no visible global function definition for ‘unmethylated’ adjustedFunnorm: no visible global function definition for ‘preprocessNoob’ adjustedFunnorm: no visible global function definition for ‘mapToGenome’ adjustedFunnorm: no visible global function definition for ‘addSex’ adjustedFunnorm: no visible global function definition for ‘getSex’ adjustedFunnorm: no visible global function definition for ‘getCN’ adjustedFunnorm: no visible global function definition for ‘assay<-’ beadcount: no visible global function definition for ‘getNBeads’ beadcount: no visible global function definition for ‘getProbeInfo’ beadcount: no visible global function definition for ‘getManifestInfo’ bgIntensitySwan.methylumi: no visible global function definition for ‘colMedians’ bscon_methy: no visible global function definition for ‘intensitiesByChannel’ bscon_methy: no visible global function definition for ‘QCdata’ bscon_minfi : csp.green: no visible global function definition for ‘getRed’ bscon_minfi : csp.green: no visible global function definition for ‘getGreen’ bscon_minfi : csp.green : <anonymous>: no visible global function definition for ‘getControlAddress’ bscon_minfi : csp.red: no visible global function definition for ‘getRed’ bscon_minfi : csp.red: no visible global function definition for ‘getGreen’ bscon_minfi : csp.red : <anonymous>: no visible global function definition for ‘getControlAddress’ canno: no visible global function definition for ‘IlluminaMethylationManifest’ combo : <anonymous>: no visible global function definition for ‘QCdata’ combo: no visible global function definition for ‘QCdata<-’ dfort: no visible binding for global variable ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’ epicv2clean.gds.class: no visible global function definition for ‘chainsaw’ estimateSex: no visible global function definition for ‘head’ estimateSex: no visible binding for global variable ‘sex_coef’ estimateSex: no visible global function definition for ‘colSds’ genall: no visible global function definition for ‘head’ generateManifest: no visible binding for global variable ‘.manifest’ generateManifest: no visible global function definition for ‘getAnnotationObject’ generateManifest: no visible global function definition for ‘getAnnotation’ generateManifest: no visible global function definition for ‘getProbeInfo’ getMethylationBeadMappers2 : <anonymous>: no visible binding for global variable ‘hm27.ordering’ getMethylationBeadMappers2 : <anonymous>: no visible binding for global variable ‘hm450.ordering’ getMethylationBeadMappers2 : <anonymous>: no visible binding for '<<-' assignment to ‘epic.ordering’ getMethylationBeadMappers2 : <anonymous>: no visible binding for global variable ‘epic.ordering’ getMethylationBeadMappers2 : <anonymous>: no visible binding for '<<-' assignment to ‘epicV2.ordering’ getMethylationBeadMappers2 : <anonymous>: no visible binding for global variable ‘epicV2.ordering’ getMethylationBeadMappers2 : <anonymous>: no visible binding for global variable ‘.manifest’ getMethylationBeadMappers2 : <anonymous>: no visible binding for global variable ‘hm27.controls’ getMethylationBeadMappers2 : <anonymous>: no visible binding for global variable ‘hm450.controls’ getMethylationBeadMappers2 : <anonymous>: no visible binding for global variable ‘epic.controls’ getMethylationBeadMappers2 : <anonymous>: no visible binding for global variable ‘epicV2.controls’ getMethylumiBeta: no visible global function definition for ‘unmethylated’ getMethylumiBeta: no visible global function definition for ‘methylated’ got: no visible global function definition for ‘getProbeInfo’ lumiMethyR2: no visible global function definition for ‘methylumiR’ oxyscale: no visible global function definition for ‘betas’ oxyscale: no visible global function definition for ‘betas<-’ p_dfsfit: no visible global function definition for ‘mclapply’ pipelineIlluminaMethylation.batch: no visible binding for global variable ‘PATH_RES’ pipelineIlluminaMethylation.batch: no visible binding for global variable ‘probeAnnotationsCategory’ preprocessIlluminaMethylation: no visible binding for global variable ‘projectName’ read.manifest: no visible global function definition for ‘DNAStringSet’ read.manifest: no visible global function definition for ‘oligonucleotideFrequency’ read.manifest: no visible global function definition for ‘letterFrequency’ readEPIC: no visible binding for global variable ‘n.sd’ readPepo: no visible binding for '<<-' assignment to ‘.manifest’ uSexQNengine: no visible global function definition for ‘mclapply’ BMIQ,MethyLumiSet : <anonymous>: no visible global function definition for ‘warn’ BMIQ,MethyLumiSet: no visible global function definition for ‘betas<-’ BMIQ,MethylSet: no visible global function definition for ‘getBeta’ BMIQ,MethylSet : <anonymous>: no visible global function definition for ‘warn’ adjustedDasen,MethyLumiSet: no visible global function definition for ‘methylated’ adjustedDasen,MethyLumiSet: no visible global function definition for ‘unmethylated’ adjustedDasen,MethyLumiSet: no visible global function definition for ‘betas<-’ adjustedDasen,MethyLumiSet: no visible global function definition for ‘methylated<-’ adjustedDasen,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ adjustedDasen,MethylSet: no visible global function definition for ‘getMeth’ adjustedDasen,MethylSet: no visible global function definition for ‘getUnmeth’ adjustedDasen,MethylSet: no visible global function definition for ‘getAnnotation’ adjustedDasen,MethylSet: no visible global function definition for ‘MethylSet’ adjustedDasen,MethylSet: no visible global function definition for ‘colData’ adjustedDasen,MethylSet: no visible global function definition for ‘metadata’ adjustedDasen,RGChannelSet: no visible global function definition for ‘preprocessRaw’ agep,MethylSet: no visible global function definition for ‘getBeta’ as.methylumi,MethyLumiSet: no visible global function definition for ‘methylated’ as.methylumi,MethyLumiSet: no visible global function definition for ‘unmethylated’ as.methylumi,MethyLumiSet: no visible global function definition for ‘betas’ as.methylumi,MethyLumiSet: no visible global function definition for ‘pvals’ as.methylumi,MethyLumiSet: no visible global function definition for ‘QCdata’ as.methylumi,MethylSet: no visible global function definition for ‘getMeth’ as.methylumi,MethylSet: no visible global function definition for ‘getUnmeth’ as.methylumi,MethylSet: no visible global function definition for ‘getBeta’ as.methylumi,MethylSet: no visible global function definition for ‘getAnnotation’ betaqn,MethyLumiSet: no visible global function definition for ‘betas<-’ betaqn,MethyLumiSet: no visible global function definition for ‘betas’ betaqn,MethylSet: no visible global function definition for ‘getBeta’ betaqn,RGChannelSet: no visible global function definition for ‘getBeta’ colnames,MethyLumiSet: no visible global function definition for ‘methylated’ danen,MethyLumiSet: no visible global function definition for ‘methylated’ danen,MethyLumiSet: no visible global function definition for ‘unmethylated’ danen,MethyLumiSet: no visible global function definition for ‘betas<-’ danen,MethyLumiSet: no visible global function definition for ‘methylated<-’ danen,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ danen,MethylSet: no visible global function definition for ‘getMeth’ danen,MethylSet: no visible global function definition for ‘getUnmeth’ danen,MethylSet: no visible global function definition for ‘MethylSet’ danen,MethylSet: no visible global function definition for ‘colData’ danen,MethylSet: no visible global function definition for ‘metadata’ danen,RGChannelSet: no visible global function definition for ‘preprocessRaw’ danes,MethyLumiSet: no visible global function definition for ‘methylated’ danes,MethyLumiSet: no visible global function definition for ‘unmethylated’ danes,MethyLumiSet: no visible global function definition for ‘betas<-’ danes,MethyLumiSet: no visible global function definition for ‘methylated<-’ danes,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ danes,MethylSet: no visible global function definition for ‘getMeth’ danes,MethylSet: no visible global function definition for ‘getUnmeth’ danes,MethylSet: no visible global function definition for ‘MethylSet’ danes,MethylSet: no visible global function definition for ‘colData’ danes,MethylSet: no visible global function definition for ‘metadata’ danes,RGChannelSet: no visible global function definition for ‘preprocessRaw’ danet,MethyLumiSet: no visible global function definition for ‘methylated’ danet,MethyLumiSet: no visible global function definition for ‘unmethylated’ danet,MethyLumiSet: no visible global function definition for ‘betas<-’ danet,MethyLumiSet: no visible global function definition for ‘methylated<-’ danet,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ danet,MethylSet: no visible global function definition for ‘getMeth’ danet,MethylSet: no visible global function definition for ‘getUnmeth’ danet,MethylSet: no visible global function definition for ‘MethylSet’ danet,MethylSet: no visible global function definition for ‘colData’ danet,MethylSet: no visible global function definition for ‘metadata’ danet,RGChannelSet: no visible global function definition for ‘preprocessRaw’ dasen,MethyLumiSet: no visible global function definition for ‘methylated’ dasen,MethyLumiSet: no visible global function definition for ‘unmethylated’ dasen,MethyLumiSet: no visible global function definition for ‘betas<-’ dasen,MethyLumiSet: no visible global function definition for ‘methylated<-’ dasen,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ dasen,MethylSet: no visible global function definition for ‘getMeth’ dasen,MethylSet: no visible global function definition for ‘getUnmeth’ dasen,MethylSet: no visible global function definition for ‘MethylSet’ dasen,MethylSet: no visible global function definition for ‘colData’ dasen,MethylSet: no visible global function definition for ‘metadata’ dasen,RGChannelSet: no visible global function definition for ‘preprocessRaw’ daten1,MethyLumiSet: no visible global function definition for ‘methylated’ daten1,MethyLumiSet: no visible global function definition for ‘unmethylated’ daten1,MethyLumiSet: no visible global function definition for ‘betas<-’ daten1,MethyLumiSet: no visible global function definition for ‘methylated<-’ daten1,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ daten1,MethylSet: no visible global function definition for ‘getMeth’ daten1,MethylSet: no visible global function definition for ‘getUnmeth’ daten1,MethylSet: no visible global function definition for ‘MethylSet’ daten1,MethylSet: no visible global function definition for ‘colData’ daten1,MethylSet: no visible global function definition for ‘metadata’ daten1,RGChannelSet: no visible global function definition for ‘preprocessRaw’ daten2,MethyLumiSet: no visible global function definition for ‘methylated’ daten2,MethyLumiSet: no visible global function definition for ‘unmethylated’ daten2,MethyLumiSet: no visible global function definition for ‘betas<-’ daten2,MethyLumiSet: no visible global function definition for ‘methylated<-’ daten2,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ daten2,MethylSet: no visible global function definition for ‘getMeth’ daten2,MethylSet: no visible global function definition for ‘getUnmeth’ daten2,MethylSet: no visible global function definition for ‘MethylSet’ daten2,MethylSet: no visible global function definition for ‘colData’ daten2,MethylSet: no visible global function definition for ‘metadata’ daten2,RGChannelSet: no visible global function definition for ‘preprocessRaw’ dmrse,MethylSet: no visible global function definition for ‘getBeta’ dmrse,MethylSet: no visible global function definition for ‘head’ dmrse,RGChannelSet: no visible global function definition for ‘getBeta’ dmrse,RGChannelSet: no visible global function definition for ‘head’ dmrse_col,MethylSet: no visible global function definition for ‘getBeta’ dmrse_col,MethylSet: no visible global function definition for ‘head’ dmrse_col,RGChannelSet: no visible global function definition for ‘getBeta’ dmrse_col,RGChannelSet: no visible global function definition for ‘head’ dmrse_row,MethylSet: no visible global function definition for ‘getBeta’ dmrse_row,MethylSet: no visible global function definition for ‘head’ dmrse_row,RGChannelSet: no visible global function definition for ‘getBeta’ dmrse_row,RGChannelSet: no visible global function definition for ‘head’ estimateCellCounts.wateRmelon,MethylSet: no visible global function definition for ‘getManifest’ estimateCellCounts.wateRmelon,MethylSet: no visible global function definition for ‘getMeth’ estimateCellCounts.wateRmelon,MethylSet: no visible global function definition for ‘getUnmeth’ estimateCellCounts.wateRmelon,MethylSet: no visible global function definition for ‘getBeta’ estimateCellCounts.wateRmelon,RGChannelSet: no visible global function definition for ‘getManifest’ estimateCellCounts.wateRmelon,RGChannelSet: no visible global function definition for ‘preprocessRaw’ estimateCellCounts.wateRmelon,RGChannelSet: no visible global function definition for ‘getMeth’ estimateCellCounts.wateRmelon,RGChannelSet: no visible global function definition for ‘getUnmeth’ estimateCellCounts.wateRmelon,RGChannelSet: no visible global function definition for ‘getBeta’ fuks,MethyLumiSet: no visible global function definition for ‘betas<-’ fuks,MethyLumiSet: no visible global function definition for ‘betas’ fuks,MethylSet: no visible global function definition for ‘getBeta’ fuks,RGChannelSet: no visible global function definition for ‘preprocessRaw’ fuks,RGChannelSet: no visible global function definition for ‘getBeta’ genki,MethyLumiSet: no visible global function definition for ‘betas’ genki,MethylSet: no visible global function definition for ‘getBeta’ genki,RGChannelSet: no visible global function definition for ‘getSnpBeta’ nanes,MethyLumiSet: no visible global function definition for ‘methylated’ nanes,MethyLumiSet: no visible global function definition for ‘unmethylated’ nanes,MethyLumiSet: no visible global function definition for ‘betas<-’ nanes,MethyLumiSet: no visible global function definition for ‘methylated<-’ nanes,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ nanes,MethylSet: no visible global function definition for ‘getMeth’ nanes,MethylSet: no visible global function definition for ‘getUnmeth’ nanes,MethylSet: no visible global function definition for ‘MethylSet’ nanes,MethylSet: no visible global function definition for ‘colData’ nanes,MethylSet: no visible global function definition for ‘metadata’ nanes,RGChannelSet: no visible global function definition for ‘preprocessRaw’ nanet,MethyLumiSet: no visible global function definition for ‘methylated’ nanet,MethyLumiSet: no visible global function definition for ‘unmethylated’ nanet,MethyLumiSet: no visible global function definition for ‘betas<-’ nanet,MethyLumiSet: no visible global function definition for ‘methylated<-’ nanet,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ nanet,MethylSet: no visible global function definition for ‘getMeth’ nanet,MethylSet: no visible global function definition for ‘getUnmeth’ nanet,MethylSet: no visible global function definition for ‘MethylSet’ nanet,MethylSet: no visible global function definition for ‘colData’ nanet,MethylSet: no visible global function definition for ‘metadata’ nanet,RGChannelSet: no visible global function definition for ‘preprocessRaw’ nasen,MethyLumiSet: no visible global function definition for ‘methylated’ nasen,MethyLumiSet: no visible global function definition for ‘unmethylated’ nasen,MethyLumiSet: no visible global function definition for ‘betas<-’ nasen,MethyLumiSet: no visible global function definition for ‘methylated<-’ nasen,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ nasen,MethylSet: no visible global function definition for ‘getMeth’ nasen,MethylSet: no visible global function definition for ‘getUnmeth’ nasen,MethylSet: no visible global function definition for ‘MethylSet’ nasen,MethylSet: no visible global function definition for ‘colData’ nasen,MethylSet: no visible global function definition for ‘metadata’ nasen,RGChannelSet: no visible global function definition for ‘preprocessRaw’ naten,MethyLumiSet: no visible global function definition for ‘methylated’ naten,MethyLumiSet: no visible global function definition for ‘unmethylated’ naten,MethyLumiSet: no visible global function definition for ‘betas<-’ naten,MethyLumiSet: no visible global function definition for ‘methylated<-’ naten,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ naten,MethylSet: no visible global function definition for ‘getMeth’ naten,MethylSet: no visible global function definition for ‘getUnmeth’ naten,MethylSet: no visible global function definition for ‘MethylSet’ naten,MethylSet: no visible global function definition for ‘colData’ naten,MethylSet: no visible global function definition for ‘metadata’ naten,RGChannelSet: no visible global function definition for ‘preprocessRaw’ outlyx,MethyLumiSet: no visible global function definition for ‘betas’ outlyx,MethylSet: no visible global function definition for ‘getBeta’ outlyx,RGChannelSet: no visible global function definition for ‘getBeta’ pfilter,MethyLumiSet: no visible global function definition for ‘betas’ pfilter,MethyLumiSet: no visible global function definition for ‘methylated’ pfilter,MethyLumiSet: no visible global function definition for ‘unmethylated’ pfilter,MethyLumiSet: no visible global function definition for ‘pvals’ pfilter,RGChannelSetExtended: no visible binding for global variable ‘RGChannelSetExtended’ pfilter,RGChannelSetExtended: no visible global function definition for ‘preprocessRaw’ pfilter,RGChannelSetExtended: no visible global function definition for ‘detectionP’ pfilter,RGChannelSetExtended: no visible global function definition for ‘subsetByLoci’ pwod,MethyLumiSet: no visible global function definition for ‘betas’ pwod,MethyLumiSet: no visible global function definition for ‘betas<-’ pwod,MethylSet: no visible global function definition for ‘getBeta’ pwod,RGChannelSet: no visible global function definition for ‘getBeta’ seabi,MethyLumiSet: no visible global function definition for ‘betas’ seabi,MethylSet: no visible global function definition for ‘getBeta’ seabi,RGChannelSet: no visible global function definition for ‘getBeta’ smokp,MethylSet: no visible global function definition for ‘getBeta’ swan,MethyLumiSet: no visible global function definition for ‘methylated’ swan,MethyLumiSet: no visible global function definition for ‘unmethylated’ swan,MethyLumiSet: no visible global function definition for ‘intensitiesByChannel’ swan,MethyLumiSet: no visible global function definition for ‘QCdata’ swan,MethyLumiSet: no visible global function definition for ‘getBeta’ swan,MethyLumiSet: no visible global function definition for ‘getMeth’ swan,MethyLumiSet: no visible global function definition for ‘getUnmeth’ swan,MethyLumiSet: no visible global function definition for ‘betas’ swan,RGChannelSet: no visible global function definition for ‘preprocessSWAN’ tost,MethyLumiSet: no visible global function definition for ‘methylated’ tost,MethyLumiSet: no visible global function definition for ‘betas<-’ tost,MethyLumiSet: no visible global function definition for ‘unmethylated’ tost,MethyLumiSet: no visible global function definition for ‘pvals’ tost,RGChannelSet: no visible global function definition for ‘detectionP’ tost,RGChannelSet: no visible global function definition for ‘preprocessRaw’ tost,RGChannelSet: no visible global function definition for ‘getMeth’ tost,RGChannelSet: no visible global function definition for ‘getUnmeth’ uSexQN,MethyLumiSet: no visible global function definition for ‘methylated’ uSexQN,MethyLumiSet: no visible global function definition for ‘unmethylated’ uSexQN,MethyLumiSet: no visible global function definition for ‘betas<-’ uSexQN,MethyLumiSet: no visible global function definition for ‘methylated<-’ uSexQN,MethyLumiSet: no visible global function definition for ‘unmethylated<-’ uSexQN,MethylSet: no visible global function definition for ‘getMeth’ uSexQN,MethylSet: no visible global function definition for ‘getUnmeth’ uSexQN,MethylSet: no visible global function definition for ‘getAnnotation’ uSexQN,MethylSet: no visible global function definition for ‘MethylSet’ uSexQN,MethylSet: no visible global function definition for ‘colData’ uSexQN,MethylSet: no visible global function definition for ‘metadata’ uSexQN,RGChannelSet: no visible global function definition for ‘preprocessRaw’ Undefined global functions or variables: .manifest .mclapply DNAStringSet IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaMethylationManifest MethylSet PATH_RES QCdata QCdata<- RGChannelSetExtended addSex assay<- assays betas betas<- chainsaw colCummaxs colData colMeans2 colMedians colQuantiles colSds detectionP epic.controls epic.ordering epicV2.controls epicV2.ordering getAnnotation getAnnotationObject getBeta getCN getControlAddress getGreen getManifest getManifestInfo getMeth getNBeads getOOB getProbeInfo getProbeType getRed getSex getSnpBeta getUnmeth head hm27.controls hm27.ordering hm450.controls hm450.ordering intensitiesByChannel letterFrequency mapToGenome mclapply metadata methylated methylated<- methylumiR n.sd oligonucleotideFrequency preprocessNoob preprocessRaw preprocessSWAN probeAnnotationsCategory projectName pvals rowMeans2 seqnames sex_coef subsetByLoci unmethylated unmethylated<- warn Consider adding importFrom("utils", "head") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) combo.Rd:24: Lost braces; missing escapes or markup? 24 | and \code{phenoData} are joined on \code{sampleName} . \code{featureData} and {annotation} are taken from | ^ * checking Rd metadata ... WARNING Rd files with duplicated alias 'NChannelSetToMethyLumiSet2': ‘NChannelSetToMethyLumiSet2.Rd’ ‘wm_internal.Rd’ Rd files with duplicated alias 'fot': ‘dot-getManifestString.Rd’ ‘got.Rd’ Rd files with duplicated alias 'got': ‘dot-getManifestString.Rd’ ‘got.Rd’ * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented data sets: ‘ageCoefs’ ‘epicV2.controls’ ‘sex_coef’ Undocumented S4 methods: generic 'adjustedDasen' and siglist 'MethyLumiSet' generic 'adjustedDasen' and siglist 'MethylSet' generic 'adjustedDasen' and siglist 'RGChannelSet' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'readEPIC.Rd': readEPIC Code: function(idatPath, barcodes = NULL, pdat = NULL, parallel = F, n = T, oob = F, force = F, two = TRUE, ...) Docs: function(idatPath, barcodes = NULL, pdat = NULL, parallel = F, n = T, oob = F, force = F, ...) Argument names in code not in docs: two Mismatches in argument names: Position: 8 Code: two Docs: ... * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'canno.Rd' ‘name’ Undocumented arguments in Rd file 'dot-createAnnotation.Rd' ‘object’ Documented arguments not in \usage in Rd file 'dot-getManifestString.Rd': ‘x’ ‘obj’ ‘fd’ ‘rn’ Undocumented arguments in Rd file 'epicv2clean.default.Rd' ‘x’ Undocumented arguments in Rd file 'readPepo.Rd' ‘oob’ Documented arguments not in \usage in Rd file 'readPepo.Rd': ‘keep’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... NOTE Argument items with no description in Rd file 'read.manifest.Rd': ‘file’ Argument items with no description in Rd file 'wm_internal.Rd': ‘mats’ ‘chans’ ‘parallel’ ‘protocol.data’ ‘IDAT’ ‘force’ * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed adjustedDasen 15.980 0.809 16.904 sextest 5.951 0.234 6.186 seabi 5.244 0.038 5.351 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 5 WARNINGs, 5 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/wateRmelon.Rcheck/00check.log’ for details.
wateRmelon.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL wateRmelon ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘wateRmelon’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ Creating a generic function from function ‘as.methylumi’ in package ‘wateRmelon’ Creating a generic function from function ‘smokp’ in package ‘wateRmelon’ Creating a generic function from function ‘adjustedDasen’ in package ‘wateRmelon’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** testing if installed package can be loaded from final location No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** testing if installed package keeps a record of temporary installation path * DONE (wateRmelon)
wateRmelon.Rcheck/wateRmelon-Ex.timings
name | user | system | elapsed | |
BMIQ | 0 | 0 | 0 | |
adjustedDasen | 15.980 | 0.809 | 16.904 | |
adjustedFunnorm | 0 | 0 | 0 | |
agep | 0.195 | 0.031 | 0.228 | |
bscon | 0.113 | 0.004 | 0.117 | |
combo | 0.317 | 0.025 | 0.342 | |
dasen | 1.002 | 0.215 | 1.218 | |
dmrse | 0.990 | 0.158 | 1.150 | |
estimateSex | 2.212 | 0.021 | 2.240 | |
genki | 1.231 | 0.306 | 1.541 | |
iDMR | 0.001 | 0.003 | 0.005 | |
melon | 0.139 | 0.005 | 0.146 | |
metrics | 3.540 | 0.193 | 3.738 | |
outlyx | 0.418 | 0.006 | 0.426 | |
pfilter | 0.183 | 0.007 | 0.190 | |
pwod | 0.439 | 0.016 | 0.455 | |
qual | 0.975 | 0.132 | 1.108 | |
readEPIC | 0 | 0 | 0 | |
seabi | 5.244 | 0.038 | 5.351 | |
sextest | 5.951 | 0.234 | 6.186 | |
smokp | 0.118 | 0.007 | 0.124 | |